{"id":"https://openalex.org/W1982309045","doi":"https://doi.org/10.1007/s10822-013-9663-5","title":"eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands","display_name":"eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands","publication_year":2013,"publication_date":"2013-06-01","ids":{"openalex":"https://openalex.org/W1982309045","doi":"https://doi.org/10.1007/s10822-013-9663-5","mag":"1982309045","pmid":"https://pubmed.ncbi.nlm.nih.gov/23838840"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-013-9663-5","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-013-9663-5","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033579800","display_name":"Micha\u0142 Bryli\u0144ski","orcid":"https://orcid.org/0000-0002-6204-2869"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michal Brylinski","raw_affiliation_strings":["Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. michal@brylinski.org","Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. michal@brylinski.org","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA","institution_ids":["https://openalex.org/I121820613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064973035","display_name":"Wei P. Feinstein","orcid":null},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei P. Feinstein","raw_affiliation_strings":["Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA","institution_ids":["https://openalex.org/I121820613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5033579800"],"corresponding_institution_ids":["https://openalex.org/I121820613"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":3.5934,"has_fulltext":false,"cited_by_count":74,"citation_normalized_percentile":{"value":0.93337337,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"27","issue":"6","first_page":"551","last_page":"567"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.7741217613220215},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6050572395324707},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5479975342750549},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.5118672251701355},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44007137417793274},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.42215052247047424},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3883568048477173},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33721569180488586},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32731881737709045},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.30428290367126465},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.27963078022003174},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.276381254196167},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17967429757118225},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14449024200439453}],"concepts":[{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.7741217613220215},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6050572395324707},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5479975342750549},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.5118672251701355},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44007137417793274},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.42215052247047424},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3883568048477173},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33721569180488586},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32731881737709045},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.30428290367126465},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27963078022003174},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.276381254196167},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17967429757118225},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14449024200439453}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1007/s10822-013-9663-5","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-013-9663-5","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:23838840","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23838840","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of computer-aided molecular design","raw_type":null},{"id":"pmh:oai:digitalcommons.lsu.edu:biosci_pubs-1656","is_oa":false,"landing_page_url":"https://digitalcommons.lsu.edu/biosci_pubs/657","pdf_url":null,"source":{"id":"https://openalex.org/S4210169993","display_name":"Civil War Book Review","issn_l":"1528-6592","issn":["1528-6592"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310315936","host_organization_name":"Louisiana State University","host_organization_lineage":["https://openalex.org/P4310315936"],"host_organization_lineage_names":["Louisiana State University"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"},{"id":"pmh:oai:repository.lsu.edu:biosci_pubs-1656","is_oa":false,"landing_page_url":"https://repository.lsu.edu/biosci_pubs/657","pdf_url":null,"source":{"id":"https://openalex.org/S4210169993","display_name":"Civil War Book Review","issn_l":"1528-6592","issn":["1528-6592"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310315936","host_organization_name":"Louisiana State University","host_organization_lineage":["https://openalex.org/P4310315936"],"host_organization_lineage_names":["Louisiana State University"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W144503896","https://openalex.org/W1527927437","https://openalex.org/W1536552954","https://openalex.org/W1543773936","https://openalex.org/W1570448133","https://openalex.org/W1571577887","https://openalex.org/W1975503985","https://openalex.org/W1975551833","https://openalex.org/W1978486653","https://openalex.org/W1981021538","https://openalex.org/W1997037174","https://openalex.org/W1997199912","https://openalex.org/W2000588380","https://openalex.org/W2001260032","https://openalex.org/W2004175162","https://openalex.org/W2006481713","https://openalex.org/W2013616490","https://openalex.org/W2015398447","https://openalex.org/W2021904716","https://openalex.org/W2032949433","https://openalex.org/W2033017177","https://openalex.org/W2033496784","https://openalex.org/W2034671873","https://openalex.org/W2036149515","https://openalex.org/W2037312364","https://openalex.org/W2047497909","https://openalex.org/W2049961577","https://openalex.org/W2052791761","https://openalex.org/W2058463742","https://openalex.org/W2059215264","https://openalex.org/W2060797027","https://openalex.org/W2062693912","https://openalex.org/W2063725620","https://openalex.org/W2065283382","https://openalex.org/W2067852761","https://openalex.org/W2072284383","https://openalex.org/W2074231493","https://openalex.org/W2080167197","https://openalex.org/W2082972649","https://openalex.org/W2083854815","https://openalex.org/W2090649877","https://openalex.org/W2091563009","https://openalex.org/W2093519758","https://openalex.org/W2096729078","https://openalex.org/W2097555181","https://openalex.org/W2103017472","https://openalex.org/W2105902442","https://openalex.org/W2106765551","https://openalex.org/W2110115297","https://openalex.org/W2111078532","https://openalex.org/W2112109058","https://openalex.org/W2112284439","https://openalex.org/W2116703791","https://openalex.org/W2116806749","https://openalex.org/W2118526609","https://openalex.org/W2118737745","https://openalex.org/W2120251063","https://openalex.org/W2122849532","https://openalex.org/W2123440974","https://openalex.org/W2126016150","https://openalex.org/W2127553917","https://openalex.org/W2127563440","https://openalex.org/W2127924375","https://openalex.org/W2130479394","https://openalex.org/W2132620282","https://openalex.org/W2134153749","https://openalex.org/W2139373949","https://openalex.org/W2139445777","https://openalex.org/W2144258433","https://openalex.org/W2145268834","https://openalex.org/W2149997286","https://openalex.org/W2151831732","https://openalex.org/W2153153865","https://openalex.org/W2153613893","https://openalex.org/W2154715418","https://openalex.org/W2161151688","https://openalex.org/W2162052906","https://openalex.org/W2164088236","https://openalex.org/W2165232124","https://openalex.org/W2168667184","https://openalex.org/W2170146596","https://openalex.org/W2189421927","https://openalex.org/W2217901364","https://openalex.org/W2236022709"],"related_works":["https://openalex.org/W1741740882","https://openalex.org/W2050330741","https://openalex.org/W2253761889","https://openalex.org/W2123053169","https://openalex.org/W2181585194","https://openalex.org/W3149404221","https://openalex.org/W1493412556","https://openalex.org/W2111643578","https://openalex.org/W2802527233","https://openalex.org/W1504467230"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
